Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005446.1 Hibiscus syriacus cultivar Beakdansim tig00012479_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57091
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:4039 original size:18 final size:19
Alignment explanation
Indices: 3993--4048 Score: 78
Period size: 18 Copynumber: 2.9 Consensus size: 19
3983 AGAGGGTTCC
3993 AGTGGTCCTTCGGGACATGT
1 AGTGGTCCTTCGGGACA-GT
*
4013 ACATGGTCCTTCGGGACA-T
1 A-GTGGTCCTTCGGGACAGT
4032 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
4049 AATATTCGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 15 0.45
19 2 0.06
20 1 0.03
21 15 0.45
ACGTcount: A:0.18, C:0.23, G:0.32, T:0.27
Consensus pattern (19 bp):
AGTGGTCCTTCGGGACAGT
Found at i:4641 original size:22 final size:22
Alignment explanation
Indices: 4610--4654 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
4600 ATAGCAGTAT
*
4610 TGTAGCAGGGGAATCGGTTCCC
1 TGTAGCAGGGGAATCAGTTCCC
*
4632 TGTAGTAGGGGAATCAGTTCCC
1 TGTAGCAGGGGAATCAGTTCCC
4654 T
1 T
4655 ATTTGCAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.27
Consensus pattern (22 bp):
TGTAGCAGGGGAATCAGTTCCC
Found at i:9652 original size:14 final size:14
Alignment explanation
Indices: 9633--9669 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
9623 ACAGAGTCCA
*
9633 AAAGGCATTCTTCG
1 AAAGGCATACTTCG
9647 AAAGGCATACTTCG
1 AAAGGCATACTTCG
9661 AAAGGCATA
1 AAAGGCATA
9670 AGTGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.22
Consensus pattern (14 bp):
AAAGGCATACTTCG
Found at i:16489 original size:4 final size:4
Alignment explanation
Indices: 16474--16544 Score: 70
Period size: 4 Copynumber: 16.5 Consensus size: 4
16464 AAGACAACAG
* *
16474 AATA AGATA AATA AATA AATAA AATA GAAAA AATA AATA AATC AATA AATA
1 AATA A-ATA AATA AATA AAT-A AATA -AATA AATA AATA AATA AATA AATA
*
16525 AAGAA AATAA AATA AATA AA
1 AA-TA AAT-A AATA AATA AA
16545 CAAAACGAAG
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
4 38 0.68
5 18 0.32
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (4 bp):
AATA
Found at i:16509 original size:18 final size:17
Alignment explanation
Indices: 16474--16549 Score: 73
Period size: 18 Copynumber: 4.4 Consensus size: 17
16464 AAGACAACAG
* *
16474 AATAAGATAAATAAATA
1 AATAAAATAAAAAAATA
16491 AATAAAATAGAAAAAATA
1 AATAAAATA-AAAAAATA
* *
16509 AAT-AAATCAATAAATA
1 AATAAAATAAAAAAATA
*
16525 AAGAAAATAAAATAAATA
1 AATAAAATAAAA-AAATA
*
16543 AACAAAA
1 AATAAAA
16550 CGAAGGGAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
16 9 0.19
17 18 0.38
18 21 0.44
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.18
Consensus pattern (17 bp):
AATAAAATAAAAAAATA
Found at i:16520 original size:26 final size:25
Alignment explanation
Indices: 16480--16544 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 25
16470 ACAGAATAAG
16480 ATAAATAAATAAATAAAATAGAA-AAA
1 ATAAATAAATAAAT-AAATA-AAGAAA
*
16506 ATAAATAAATCAATAAATAAAGAAA
1 ATAAATAAATAAATAAATAAAGAAA
16531 ATAAAATAAATAAA
1 AT-AAATAAATAAA
16545 CAAAACGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 2 0.06
25 10 0.29
26 23 0.66
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (25 bp):
ATAAATAAATAAATAAATAAAGAAA
Found at i:16521 original size:30 final size:30
Alignment explanation
Indices: 16435--16544 Score: 98
Period size: 30 Copynumber: 3.6 Consensus size: 30
16425 TGGAGATTAT
** * *
16435 GAAAATAAAAGGAATATATAAAAAAAATAAA
1 GAAAATAAAATAAATAAAT-AAATAAATAAA
* * *
16466 GACAACAGAATAAGATAAATAAATAAATAAA
1 GAAAATAAAATAA-ATAAATAAATAAATAAA
*
16497 -ATAGAA-AAAATAAATAAATCAATAAATAAA
1 GA-A-AATAAAATAAATAAATAAATAAATAAA
16527 GAAAATAAAATAAATAAA
1 GAAAATAAAATAAATAAA
16545 CAAAACGAAG
Statistics
Matches: 64, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
29 2 0.03
30 30 0.47
31 25 0.39
32 7 0.11
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (30 bp):
GAAAATAAAATAAATAAATAAATAAATAAA
Found at i:18285 original size:106 final size:106
Alignment explanation
Indices: 18100--18525 Score: 721
Period size: 106 Copynumber: 4.0 Consensus size: 106
18090 TGTATTGTTC
* * *
18100 CGAGTCCAATATCC-TCTGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTC-GCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
18164 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
18206 CGAGTCCAATATTCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
18271 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGATGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
*
18312 CGAGTCCAAT-GCCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATCC-TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
18376 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
18418 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* *
18483 ACCAGTCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
18524 CG
1 CG
18526 GGTGGCACGA
Statistics
Matches: 303, Mismatches: 14, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
105 1 0.00
106 298 0.98
107 4 0.01
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.35
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:19975 original size:18 final size:18
Alignment explanation
Indices: 19948--19983 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
19938 TGTTGAATCC
*
19948 CCAAAGATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
19966 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
19984 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:21067 original size:21 final size:19
Alignment explanation
Indices: 21050--21106 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
21040 TTCCTTTTGA
21050 TTTTTGCTTCTTTTCTTTT
1 TTTTTGCTTCTTTTCTTTT
* * *
21069 TTGTT-CTTGTTTT-TTCT
1 TTTTTGCTTCTTTTCTTTT
21086 TTTTTGCTTCTTTTCTTTT
1 TTTTTGCTTCTTTTCTTTT
21105 TT
1 TT
21107 GTTCTTGATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
17 7 0.23
18 14 0.47
19 9 0.30
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (19 bp):
TTTTTGCTTCTTTTCTTTT
Found at i:21075 original size:15 final size:16
Alignment explanation
Indices: 21050--21112 Score: 74
Period size: 16 Copynumber: 3.8 Consensus size: 16
21040 TTCCTTTTGA
21050 TTTTTGCTTCTTTTCT
1 TTTTTGCTTCTTTTCT
*
21066 TTTTTGTTCTTGTTTTTTCT
1 TTTTTG--C-T-TCTTTTCT
21086 TTTTTGCTTCTTTTCT
1 TTTTTGCTTCTTTTCT
21102 TTTTTG-TTCTT
1 TTTTTGCTTCTT
21113 GATTGAATCT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
15 5 0.12
16 19 0.46
17 1 0.02
18 2 0.05
19 1 0.02
20 13 0.32
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (16 bp):
TTTTTGCTTCTTTTCT
Found at i:21112 original size:10 final size:10
Alignment explanation
Indices: 21062--21099 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
21052 TTTGCTTCTT
21062 TTCTTTTTTG
1 TTCTTTTTTG
21072 TTCTTGTTTT-
1 TTCTT-TTTTG
21082 TTCTTTTTTG
1 TTCTTTTTTG
21092 CTTCTTTT
1 -TTCTTTT
21100 CTTTTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.16
10 10 0.40
11 11 0.44
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (10 bp):
TTCTTTTTTG
Found at i:24585 original size:10 final size:10
Alignment explanation
Indices: 24566--24620 Score: 67
Period size: 10 Copynumber: 5.4 Consensus size: 10
24556 ACAGTTAGTA
24566 AAATAAAAAT
1 AAATAAAAAT
*
24576 AAATAGAAAT
1 AAATAAAAAT
24586 AAATAAAAAT
1 AAATAAAAAT
*
24596 AAATAATAAT
1 AAATAAAAAT
24606 -AATAGTAAAAT
1 AAATA--AAAAT
24617 AAAT
1 AAAT
24621 GGCAAGAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
9 4 0.11
10 27 0.71
11 4 0.11
12 3 0.08
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:25873 original size:2 final size:2
Alignment explanation
Indices: 25866--25892 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25856 CAATAACGTA
25866 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
25893 ACATATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27050 original size:12 final size:11
Alignment explanation
Indices: 27013--27064 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
27003 TATTATAAAA
27013 TATATTTTTAT
1 TATATTTTTAT
* *
27024 TATAATTATAAT
1 TAT-ATTTTTAT
27036 TATATTTTTAT
1 TATATTTTTAT
27047 T-TATATTTT-T
1 TATAT-TTTTAT
27057 TATATTTT
1 TATATTTT
27065 AAATTTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
10 8 0.24
11 17 0.50
12 9 0.26
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TATATTTTTAT
Found at i:27059 original size:13 final size:12
Alignment explanation
Indices: 27013--27056 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
27003 TATTATAAAA
27013 TATATTTTTA-T
1 TATATTTTTATT
* * *
27024 TATAATTATAAT
1 TATATTTTTATT
27036 TATATTTTTATT
1 TATATTTTTATT
27048 TATATTTTT
1 TATATTTTT
27057 TATATTTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 8 0.30
12 19 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATATTTTTATT
Found at i:28381 original size:4 final size:4
Alignment explanation
Indices: 28372--28396 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
28362 TTCAAACTAG
28372 CATT CATT CATT CATT CATT CATT C
1 CATT CATT CATT CATT CATT CATT C
28397 TATAGAACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (4 bp):
CATT
Found at i:39644 original size:20 final size:20
Alignment explanation
Indices: 39619--39709 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 20
39609 TAAATTAAAT
*
39619 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
39639 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
39659 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
39671 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
39691 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
39710 TATTCTGTTG
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.07
17 3 0.06
18 1 0.02
19 2 0.04
20 38 0.70
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:44244 original size:20 final size:20
Alignment explanation
Indices: 44219--44302 Score: 91
Period size: 20 Copynumber: 4.0 Consensus size: 20
44209 TAAATTAAAT
*
44219 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
44239 ATTAGATAGAATCAGTTTTCTA
1 ATTAGATAGAATCAG-TTT-TA
44261 TTTTATTAGATAG-ATCA-TTTTA
1 ----ATTAGATAGAATCAGTTTTA
44283 ATTAGATAGAATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
44303 TTCTGTTGCT
Statistics
Matches: 55, Mismatches: 1, Indels: 16
0.76 0.01 0.22
Matches are distributed among these distances:
18 9 0.16
19 4 0.07
20 19 0.35
21 3 0.05
22 4 0.07
23 3 0.05
25 4 0.07
26 9 0.16
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:47710 original size:2 final size:2
Alignment explanation
Indices: 47703--47772 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
47693 CTTGATGTTA
47703 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
47745 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
47773 AAGAATATTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:51721 original size:2 final size:2
Alignment explanation
Indices: 51714--51751 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
51704 AGAAAGATGA
51714 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51752 TTGTCAGAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52080 original size:48 final size:48
Alignment explanation
Indices: 52023--52127 Score: 203
Period size: 48 Copynumber: 2.2 Consensus size: 48
52013 ACTCAGCCAC
52023 AACC-TAGCACCAGCGGTATGAATACATAACAAGACAACCTGAGCCTG
1 AACCTTAGCACCAGCGGTATGAATACATAACAAGACAACCTGAGCCTG
52070 AACCTTAGCACCAGCGGTATGAATACATAACAAGACAACCTGAGCCTG
1 AACCTTAGCACCAGCGGTATGAATACATAACAAGACAACCTGAGCCTG
52118 AACCTTAGCA
1 AACCTTAGCA
52128 TGCCATAACA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 4 0.07
48 53 0.93
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.16
Consensus pattern (48 bp):
AACCTTAGCACCAGCGGTATGAATACATAACAAGACAACCTGAGCCTG
Done.